Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an effective method for analyzing peptides and proteins and therefore has a significant role in proteomics. When samples are complex (e.g. multi-protein digests, cell lysates, tissue extracts, etc.) or when the analyte(s) of interest are in very dilute solutions, MALDI-MS analyses can be difficult. Consequently, sample cleanup methods that eliminate interferences while simultaneously providing selective extraction of the desired analytes are valuable. Numerous on-probe clean-up methods for MALDI have been developed, but most are limited to the elimination of salts and other interferences from the sample with little concentration of the sample. Some MALDI surfaces, however, have been developed that provide both sample clean-up and concentration. Alternate approaches to on-probe clean-up methods are sample preparation protocols that simultaneously purify and concentrate peptides before depositing them on the MALDI probe. These methods rely mostly on traditional chromatographic techniques or solid-liquid extractions that are driven by a variety of interactions between the analyte and the solid support. These approaches decouple the extraction and MALDI analysis steps so that both can be independently optimized.
Liquid-liquid extractions using two immiscible phases are another means by which analyte purification and concentration can be performed. Such liquid-liquid extractions are advantageous in that they provide analyte extraction, purification, and concentration in a single step. Also, analyte transport rates are faster than in liquid-solid extractions, which allow reduced extraction times, and analytes can be quickly and easily concentrated via evaporation of organic solvents. Typically, however, these liquid-liquid extractions are limited to hydrophobic analytes and have very limited potential in peptide and protein analyses unless the organic phase can be modified in some way. Accordingly, a number of shortcomings remain in the art of preparing samples for the MALDI analysis of peptides.